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Proteomics. Proteomics. Proteomics directly detects expression of proteins. . Proteome research permits the discovery of new protein markers for diagnostic purposes and of novel molecular targets for drug discovery. 1. SWISS-2DPAGE database.

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Proteomics

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Proteomics


Proteomics

  • Proteomics directly detects expression of proteins.

  • Proteome research permits the discovery of new protein markers for diagnostic purposes and of novel molecular targets for drug discovery.


1. SWISS-2DPAGE database

  • SWISS-2DPAGE is an annotated two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) database established in 1993.

  • The SWISS-2DPAGE database is maintained by the Swiss Institute of Bioinformatics, in collaboration with the Central Clinical Chemistry Laboratory of the Geneva University Hospital.


SWISS-2DPAGE Search Page


View entry in original SWISS-2DPAGE format

Entry name: VSP2_ARATH

Primary accession number:82122

Entered in SWISS-2DPAGE inRelease 13, December 2000

Last modified inRelease 14, October 2001

Name and origin of the protein: DescriptionVegetative storage protein 2.

Gene name(s)VSP2 OR AT5G24770FromArabidopsis thaliana (Mouse-ear cress). [TaxID: 3702]

TaxonomyEukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II; Brassicales; Brassicaceae; Arabidopsis.

References[1]  MAPPING ON GEL. Sarazin B., Tonella L., Marques K., Paesano S., Chane-Favre L., Sanchez J.-C., Hochstrasser D.F., Thiellement H.; Submitted (OCT-2000) to the SWISS-2DPAGE database.

2D PAGE maps for identified proteinsCompute the theoretical pI/MwHow to interpret a protein map

Arabidopsis thalianaMAP LOCATIONS: SPOT 2D-001KKV: pI=6.47, Mw=29849 *** the clicked spot ***

MAPPING: MASS SPECTROMETRY [1].


Mass spectrometry (MS)


2. PeptIdent

  • PeptIdent is a tool that allows the identification of proteins using pI, MW and peptide mass fingerprinting data. Experimentally measured, user-specified peptide masses are compared with the theoretical peptides calculated for all proteins in the SWISS-PROT/TrEMBL databases.


3. Mascot

  • Mascot is a powerful search engine that uses mass spectrometry data to identify proteins from primary sequence databases.


  • Concise Protein Summary Report

  • Switch to full Protein Summary Report

  • To create a bookmark for this report, right click this link: Concise Summary Report (../data/20020713/FATeiic.dat)

  • P82691Mass: 1011 Total score: 25 Peptides matched: 1 Pyrokinin-1 (Pea-PK-1) (FXPRL-amide)

  • P82041 Mass: 1736 Total score: 24 Peptides matched: 1 Uperin 3.4 1. 3.

  • P36396Mass: 2069 Total score: 23 Peptides matched: 1 Sex-determining region Y protein (Testis-determining factor) (Fragment)


4. FindMod

  • This tool examines peptide mass fingerprinting data for mass differences between empirical and theoretical peptides. Where mass differences correspond to a post-translational modification (PTM).


Post-translational modifications Mass values used in FindMod

  • ModificationsAbbreviationMonoisotopicAverage __

  • AcetylationACET42.010642.0373

  • AmidationAMID-0.9840-0.9847

  • Beta-methylthiolationBMTH45.987711846.08688

  • BiotinBIOT226.0776226.2934

  • CarbamylationCAM43.0058143.02502

  • CitrullinationCITR0.98402760.98476

  • C-MannosylationCMAN162.052823162.1424

  • DeamidationDEAM0.98400.9847

  • N-acyl diglyceride

  • cysteine (tripalmitate)DIAC788.7258789.3202

  • DimethylationDIMETH28.031428.0538

  • FADFAD783.1415783.542

  • FarnesylationFARN204.1878204.3556

  • FormylationFORM27.994928.0104

  • Geranyl-geranylGERA272.2504272.4741

  • Gamma-carboxyglutamic acidGGLU43.9898344.0098

  • O-GlcNAcGLCN203.0794203.1950

  • Glucosylation (Glycation)GLUC162.0528162.1424

  • HydroxylationHYDR15.994915.9994

  • LipoylLIPY188.033188.3027

  • MethylationMETH14.015714.0269

  • MyristoylationMYRI210.1984210.3598

  • PalmitoylationPALM238.2297238.4136

  • PhosphorylationPHOS79.966379.9799

  • Pyridoxal phosphatePLP229.014229.129

  • PhosphopantetheinePPAN339.078339.3234

  • Pyrrolidone carboxylic acidPYRR-17.0266-17.0306

  • SulfationSULF79.956880.0642

  • TrimethylationTRIMETH42.047142.0807


Biochemical Pathway Databases

  • Linking the biochemical pathways together and integration with the genomic data are the great tasks of biochemical pathway databases.


Metabolomics:From Genes to Pathways:


Where do we go?

“Deconstruction of biological processes into their molecular components”.


DNA (Genomics)

RNA (Transcriptomics)

Protein (Proteomics)

Metabolites (Metabolomics)


From: Gene, genome, cell, organism, population,… towardSystem Biology


What are we going to do?


Fact:Individual research units would not work any more!

Recommendation:

Team up!

Go beyond your own, your institute, and your country boundaries.


Fact:Genomic data are suppose to reduce time and efforts for preparation of reagents, resources and information.

Recommendation:

Think big!

  • Search and use data intelligently.

  • Turn attention to complex biology from various angles, i.e. have all needed specialty in your team.


Fact:A mass of data is available freely!

Recommendation:

Learn how to use!

Make use of them to develop technologies.


Fact:Biology world is rapidly changing!

Recommendation:

Keep up with changes!

  • Re-establish systems with more flexibility and more freedom.

  • Loose regulations for funding, employment, etc.

  • Re-design your research project.


Thanks for Your Attention


Cautions:

  • One protein with different roles:

    • Alpha-enolase in liver

    • T-crystallin in eye lens

  • One structure in proteins with diverse functions:

    • TIM barrels in isomerases, oxidoreductase and hydrolases.

  • 30% error in automated annotations.


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